Driver door will not completely close?

I had to put a new motor for the driver door window. I didn’t remove the old one and had a hard time putting in the new one. I’m not sure it’s in properly because the bolts holding the window to the lifting bar keeps coming off and I have taken it all apart again. This has happened maybe 8 times. So, it’s a continuing problem along with the door not completely closing so the light stays on and kills my battery. What do I do??